Foldmason not running on large set of proteins

Question

Foldmason not running on large set of proteins

Opened this issue 4 months ago · 11 comments

Expected Behavior

I am running foldmason with the command below:
easy-msa /workspace/protein/structs /workspace/results_foldmason/protein/result /workspace/results_foldmason/protein/tmpFolder --report-mode 1 --precluster --max-seq-len 4000

I have about 2000 proteins of approx length 280 amino acids.

Current Behavior

I am getting memory errors.

Steps to Reproduce (for bugs)

Just run easy-msa on a large set of sequences.

Foldseek Output (for bugs)

I get the output below (last few lines):

Size of the sequence database: 3588
Size of the alignment database: 3588
Number of clusters: 1487

Writing results 0h 0m 0s 0ms
Time for merging to clu: 0h 0m 0s 428ms
Time for processing: 0h 0m 36s 725ms
Error: structuremsa died
Segmentation fault (core dumped)

Context

The --max-seq-len parameter doesn't seem to make a difference. I'm still getting the memory error.

Your Environment

I've been running foldmason via the docker image created from the dockerfile. I am running on a kubernetes cluster and provide 64Gb of RAM, and 6 cpus.

Answer 1 · 2024-09-05T01:44:04.000Z

Do you also get the same behaviour with pre-clustering disabled (--precluster 0)?

Answer 2 · 2024-09-05T01:49:06.000Z

Yes, I see the same behavior with precluster disabled. Rasna "Success never rests. On your bad days, be good. On your good days, be great. And on every other day, get better."

…

On Sep 4, 2024 at 8:44 PM -0500, Cameron Gilchrist ***@***.***>, wrote: Do you also get the same behaviour with pre-clustering disabled (--precluster 0)? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

Answer 3 · 2024-09-05T02:09:11.000Z

How did you build the container? I just realized that we have not been automatically building containers.

Answer 4 · 2024-09-05T14:31:18.000Z

@gamcil commited a fix earlier today. Could you check if the issue is still happening for you? You can download precompiled binaries at https://mmseqs.com/foldmason.

Answer 5 · 2024-09-05T15:23:18.000Z

How did you build the container? I just realized that we have not been automatically building containers.

I used the Dockerfile provided in the repository

Answer 6 · 2024-09-05T15:42:10.000Z

@gamcil commited a fix earlier today. Could you check if the issue is still happening for you? You can download precompiled binaries at https://mmseqs.com/foldmason.

Running this now. It seems to have gone further than before. I removed --report-mode 1. Could that be causing the issue?

Answer 7 · 2024-09-05T15:56:36.000Z

@gamcil commited a fix earlier today. Could you check if the issue is still happening for you? You can download precompiled binaries at https://mmseqs.com/foldmason.

Running this now. It seems to have gone further than before. I removed --report-mode 1. Could that be causing the issue?

Confirmed that running with the precompiled binaries and using the command:
./foldmason easy-msa /workspace/protein/structs /workspace/results_foldmason/protein/result /workspace/results_foldmason/protein/tmpFolder --precluster ran without any errors. So the issue might be including the --report-mode 1 parameter.

Answer 8 · 2024-09-06T01:31:14.000Z

Were you getting segfaults also with --report-mode 1?

Answer 9 · 2024-09-06T15:33:01.000Z

Were you getting segfaults also with --report-mode 1?

It seems like the problem is --report-mode 1. If I remove that and run the command, I don't get segfaults. If I include it, I get segfaults.

Answer 10 · 2024-09-06T16:53:31.000Z

Would it be possible to share the inputs so that we can try to reproduce the new issue?

Answer 11 · 2024-09-06T22:10:34.000Z

Would it be possible to share the inputs so that we can try to reproduce the new issue?

I tried it again with --report-mode 1 and it seems to be working. Thank you for the assistance. I'll reach out in case I face any problems.